[gmx-users] Adding a new molecule

David spoel at xray.bmc.uu.se
Tue Feb 22 06:58:19 CET 2005

On Tue, 2005-02-22 at 00:11 -0500, Ramachandra Rao Gullapalli wrote:
> Hi all
> I am a beginner to MD simulations and am using gromacs to simulate a lipid
> bilayer. I tried finding information regarding this question in the archives,
> but couldnt.
> I would like to to add a different kind of lipid molecule to a DMPC lipid
> bilayer.I have built the molecule using gaussview,and used babel to convert it
> to pdb format.I now need to incorporate this in the lipid bilayer. How do i do
> this?
> Also, for a molecule which i built in gaussview, how do i build the topology
> files? do i just use pdb2gmx?

No thatä's only for proteins. Check the website of the Tieleman group
for lipid topologies.

> Thank you very much
> Regards
> Rama
> The important thing is not to stop questioning. Curiosity has its own reason for existing...
> -Einstein 
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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